They planned big for Superstorm Sandy, but not big enough. Consolidated Edison figured any surge would not surpass the 11-foot record set nearly two centuries ago. Or the design limit of 12.5 feet for a key substation in lower Manhattan. But the wall of seawater reached 14 feet. The surge that swamped the substation cut power to about 250,000 customers. It was the signature event in a series of electrical failures from winds and floods that at one point left almost 1 million Con Edison customers in the dark—a record storm outage for the utility. Con Edison planners knew by Monday evening that they would face an extraordinary mix of threats to their electrical network: a historically powerful storm, a very high tide driven by a full moon, critical electrical equipment buried under the streets, and full-force exposure to the intensity of the elements via New York Harbor, the Atlantic estuary known as the East River, and other waterways. So they prepared for a rough go. But events defied elaborate planning and expectations. The substation, located near the East River in the southeast portion of Manhattan, had withstood a surge of 9.5 feet during last year's Hurricane Irene. The utility figured the infrastructure also could handle a repeat of the highest surge on record for the area—11 feet during a hurricane in 1821, according to the National Weather Service. They also did not expect the design limit of 12.5 feet to be threatened. But as water poured into the substation Monday evening, the blinding flash of an explosion lit the most famous skyline in the world, then plunged the bottom third of Manhattan into darkness. "Nobody predicted it would be that high," said Con Edison spokesman Allan Drury. A proactive Con Edison had hoped to avoid disaster by shutting down three similar power networks in Manhattan and one in Brooklyn in advance of the storm surge. As the storm's predicted path zeroed in on the New York metropolitan area, Con Edison brought on extra work crews and laid plans to shut down some underground equipment in lower Manhattan and other parts of the city. By late Monday afternoon, the utility started to notify Manhattan customers south of 36th Street—an area encompassing nearly a third of Manhattan—that power might be shut off if underground equipment was flooded with corrosive, destructive seawater. The company gave the same heads-up to some customers in outlying Brooklyn, Queens and the Bronx. By mid-evening, though, conditions had worsened. More than 150,000 customers in New York City and the northern county of Westchester were already off grid. The utility began turning off the power, as a precaution, to a section of lower Manhattan, including Wall Street, in an attempt to stem damage. Shortly afterward, the company began cutting electricity in parts of Brooklyn too; a total of 220,000 other customers were already in the dark. Less than an hour later, more equipment flooded, sparks flew, and the blast boomed across the East River—Manhattan's eastern border—and throughout lower Manhattan from what Con Edison believes was a circuit breaker at its flooded substation. The flooded equipment had failed. When live electric equipment is inundated with salt water, electricity escapes every which way, sending sparks flying and damaging equipment. "You see a huge blast just from the short circuit," said Arshad Mansoor, senior vice president for research and development at the Electric Power Research Institute, an industry-funded research group. And the troubles didn't end as the storm slowly moved off. Con Edison said problems to its high-voltage systems caused by the hurricane forced the utility to cut power to about 160,000 customers in Brooklyn and Staten Island on Tuesday night. As day broke Tuesday, the company was busily assessing damage and fixing equipment. But downed trees and wires, as well as lingering flood waters, made it hard for repair crews to reach some areas. The utility was able to get at least 140,000 customers back on the grid within several hours, while hundreds of thousands of others hunkered down for a longer outage. Con Edison said customers served by underground equipment should be restored to service by the weekend. Those who get power from overhead lines are expected to wait longer. That's because there are so many fallen lines. The most densely populated parts of the city, generally in Manhattan and Brooklyn, are served by underground transmission wires. These offer protection from wind and falling tree limbs that plague overhead wires and make the suburbs far more vulnerable to outages. Underground wires, though, can flood and be more difficult to repair, especially in low-lying areas. It can be harder for workers to get to the wires because manholes flood. When water recedes, it can be harder to find problems, pull out wires and equipment, dry them, fix them, and slide them back into place. The damage assessment could take days to complete. To engineers like Joannes Westerink, a University of Notre Dame researcher who is working on a computer model for future New York City storm surges, this was all predictable. "You build infrastructure too low, and you run into trouble," he said. "It's a recipe for disaster." He said it's well known that New York City had spread to ever-lower zones in modern history. He cited Battery Park at the tip of Manhattan as a dramatic example. Con Edison could likely have preemptively shut more networks served by the substation that exploded, but that would have meant cutting power to tens of thousands of people and critical facilities like hospitals. Even though hospitals have backup power generators, they too can fail. Generators at New York University Langone Medical Center went down Monday night, and patients were evacuated. "You have to make the decision to shut off power to a substation very, very carefully, especially if it serves critical facilities," Mr. Mansoor said. The decision can turn into a lose-lose situation. Despite the latest damage, Mr. Mansoor called the New York City system the most reliable in the world because it's normally well protected from weather and set up with backup equipment. That protects the city from minor disruptions and helps keep major disruptions from cascading through the city. No system, he said, can be designed to withstand every storm, no matter how severe. Carol Friedland, a Louisiana State University engineer who has studied the impact of flooding on electrical systems, said more measures should be taken to protect equipment in low-lying places. For example, sea walls can be raised, and equipment can sometimes be relocated. "My personal opinion ... is that there should be more resilience built into these types of infrastructure, because when the power goes out, it disrupts the entire community," she said. Massoud Amin, a University of Minnesota electrical engineering professor who has studied power outages, said the storm underscores the need to improve the nation's electric grid by stringing more high-voltage wire and using modern sensor technology to spot problems sooner, isolate damage, and speed recovery from outages. "Our electrical infrastructure system is a marvel of engineering for the last century," Mr. Amin said. "The grid operators and the power companies are doing the best they can." It is too soon to say if anything more could have been done to keep the New York City grid working. Under state regulations, Con Edison will be required to file a report on the outage to the New York State Department of Public Service within 60 days of power restoration. That agency's staff will evaluate how problems were handled and if improvements can be made for the future, according to agency spokeswoman Pamela Carter.